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A blog from the Microbiology Society. The Microbiology Society (formerly Society for General Microbiology) is a membership organisation for scientists who work in all areas of microbiology. It is the largest learned microbiological society in Europe with a worldwide membership based in universities, industry, hospitals, research institutes and schools.

Microbe Post has a new look and has moved to the Microbiology Society’s website.

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Since 2012 Microbe Post has featured blog posts about the latest research being published in our journals, videos and podcasts about microbiology, and reported on policy updates and Society events. In 2017 the blog won the Dr Katharine Giles award for best science blog at the ABSW Science Writers’ Awards.

Microbe Post now sits on our website underneath the News tab and will continue to publish high-quality posts about the latest journal news and Society activities, as well as the New to Science series and Twitter summaries of our events.

Newly published blogs will continue to be featured on our homepage, and you can explore the blog archive and the different categories via the blog landing page.

The Journal of Medical Microbiology (JMM) is a journal published by the Microbiology Society, focused on providing a comprehensive coverage of medical, dental and veterinary microbiology and infectious diseases, including bacteriology, virology, mycology and parasitology.

Below, you can see Norman Fry’s synopsis of the paper along with a brief lay summary from the first author. The full paper is free to read for one month on the Journal of Medical Microbiology website here.

Norman Fry – Many countries are seeing a resurgence of potentially life-threatening vaccine-preventable diseases, including diphtheria, due to suboptimal levels of childhood immunisation, waning immunity, increased population movement, political instability and breakdown of healthcare and public health systems. Microbiological characterisation of isolates together with key epidemiological data informs our understanding of microbial populations and disease over time. In their article, Mohd Khalid et al. describe the characterisation of Corynebacterium diphtheriae from Malaysia to investigate a rise in cases, from an average of less than three per year since 1990 to 31 in 2016. Reports collated by the World Health Organization show that this increase in cases in Malaysia was sustained in 2017 with 32 cases. Selected isolates were characterised using phenotypic and genotypic methods including whole-genome sequencing from which multi-locus sequence typing (MLST) data were derived.

Their analyses show that the 2016 cases were caused by new clonal lineages in Malaysia. A number of novel sequence types were identified, one of which (ST453) appeared responsible for an outbreak in the state of Kedah. This article also highlights the utility of existing MLST schemes. Such schemes, together with newer core genome MLST schemes, their accompanying curated databases and bioinformatic tools such as those hosted by the PubMLST.org website, are becoming increasingly important in order to increase our understanding of the spread and transmission of these organisms.

The number of cases of diphtheria in Malaysia has remained low for nearly three decades, but this changed in 2016 when 31 cases were confirmed by the World Health Organization. To investigate this, we collected, characterised, and performed whole genome sequencing of 15 isolates from the 2016 cases and compared the results with isolates from previous isolations (1981–2010).

We showed that the 2016 cases were caused by emergence and spread of new clonal lineages in Malaysia. We also identified two clonal lineages that has persisted for more than 25 years and could potentially become an important source of diphtheria infection in the country.

In this article, Godlee et al. convincingly define the role of the Salmonella enterica ser. Typhimurium protein SrcA as a chaperone for the SPI-2 effector SteD via type 3 secretion (T3SS). This allows Salmonella to interfere with mature Major Histocompatibility Complex class II (mMHCII) expression at the plasma membrane of infected antigen-presenting cells. SrcA had previously been assigned a role as chaperone of other SPI-2 T3SS effectors, but this work refutes that idea, demonstrating that SrcA is involved in SteD stability, secretion and translocation.

During infection, Salmonella uses a type three secretion system to deliver effector proteins into host cells. Many effectors require bacterial-encoded chaperones for delivery by the secretion system. One of these effectors, called SteD, decreases antigen presentation by dendritic cells.

In this study we found that SrcA, previously proposed as a chaperone for two other effectors, is also required for this activity. We demonstrated that SrcA is a chaperone for SteD, explaining its requirement for SteD function. A direct interaction between SrcA and SteD is necessary for the stability of SteD in Salmonella and for its delivery into host cells.

To access the full paper, click here. Editor’s Choice articles published in Microbiology are free to read.

Dr. Steve Ormerod, Professor of Biosciences at Cardiff University, Co-Director of the Cardiff Water Research Institute, and Vice President of the Royal Society for the Protection of Birds (RSPB), spoke at this month’s Policy Lunchbox. In his talk on the importance of academic engagement with policy, Steve shared his personal experiences in engaging with the policy process and how other scientists can maximise their policy impact. Here, Eva Scholtus from the Microbiology Society’s Policy Team, summarises Steve’s key take-home messages for academics wanting to engage with policy-makers.

From picking a pub for a night out to deciding on the management principles of ecosystems, most of the decisions we make rest on political interactions. When it comes to nature conservation, such interactions have global ramifications. Although Steve’s research activities are explicitly ecological, solutions to the problems of freshwater ecosystems through policy are an important focus of his work. His research has influenced the policy-making and advocacy activities of a range of government bodies and major NGOs for years.

Policy beginnings

During the 1980s, acid rain was a major environmental concern. Rivers and lakes were affected over large areas of Britain, Europe and North America. Steve’s PhD focused on understanding the effects of acid rain on fresh water ecosystems and his research led to the delivery of the world’s first data revealing change effects on upland river ecosystems. At a time when Britain was known as the “dirty man of Europe” the Department for Environment used Steve’s findings to set up the acid water review group. For Steve, this marked the beginning of an exciting policy-oriented scientific career that gave him the opportunity to solve important problems.

One thing leads to another…

When sharing his experience in engaging with the policy process, Steve explained that one thing often leads to another. Under his chairmanship, the RSPB became increasingly active in the policy process and multiplied projects to promote nature conservation amongst policy-makers. Steve highlighted some key examples of when the RSPB influenced environmental decision-making:

The State of Nature report brought together data from over 50 organisations highlighting the dramatic consequences of intensive agricultural practices and climate change on the wildlife and the environment, with the UK faring worse than most other countries. This powerful consortium mobilised the media and made a compelling political point. A new report is on its way for 2019, shortly in advance of the 2020 deadline for meeting the Aichi targets, global biodiversity targets agreed under the Convention for Biological Diversity.

For the Wallasea Island Wild Coast Project, the RSBP worked with Crossrail – a British project to build major new railway connections under central London – who were seeking a beneficiary to reuse the clean spoil from their tunnelling. RSPB transformed the clay, chalk and gravel from the Crossrail partnership into 1,500 acres of tidal wildlife habitat. The Wallasea Island Wild Coast project is now a landmark conservation and engineering scheme – the largest of its type in Europe. It is also a great example of how environment regulation can enable economic activity and have a tremendous policy impact.

Wallasea Island in Essex is the site of the largest coastal habitat restoration ever undertaken in the UK.

Influencing policy by becoming a trusted public servant

In order to increase their policy impact, research scientists should be aware of the complex range of factors involved in policy interactions. Government is an obvious one; this is where most policy formulation is carried out. Less obvious are professional bodies such as the Chartered Institute of Ecology and Environmental Management, learned societies like the British Ecological Society, the civil society, and the business sector. These groups influence one another in a constant “battle of ideas”. Steve emphasised key considerations for scientists wishing to participate and influence such processes:

Research with obvious applications and a problem-solving vocation is more likely to influence policy-making than exploratory, blue-skies research;

Literature reviews are invaluable opportunities to synthesise existing information, expose knowledge gaps, and advise on how to efficiently use available evidence;

Networking and collaborating with policy organisations allow scientists to share their research and to gain a better understanding of the policy needs and regulatory contexts that they seek to inform;

Scientific research has intrinsic worth value for solving problems. Those that embrace the “public-service mentality” are in the best position to effectively influence policy-making.

Steve’s parting message for increasing policy impact is to remain scientifically objective when expressing an opinion. Throughout his career, Steve has been just as ready to give evidence to the central electricity generating board as he has been to inform the regulators of electricity generation. One thing that he has learned is that, if they maintain integrity and stay true to the evidence, research scientists can become trusted advisors capable of significantly impacting the world of policy.

The Junior Awards for Microbiology (JAM Talks) are the monthly seminar series based in Birmingham that allows early career researchers to gain experience presenting to an audience of their peers.

This month, we talked to Alice Lanne and Anja Djokic – both part of the JAM Talks Organising Committee – to discuss their involvement in the talks and their views on the importance of presenting experience for early career researchers.

To celebrate our 75th anniversary in 2020, we’re inviting members to nominate the discovery or event that best showcases why microbiology matters and helps us demonstrate the impact of microbiologists past, present and future.

With the end of 2018 fast approaching, we are taking a look back at this year’s blog posts. This year has turned out to be a great one; from fatbergs to antimicrobial resistance, we really have learnt about some amazing microbiology.

So here we go, a countdown of the top most-viewed posts from the blog this year:

This blog was written by some of our members from the University of Warwick. Frustrated by the difficulty in collecting microbial growth data in the lab, they used 3D printing techniques and basic laboratory materials to develop their own device. After they completed their design, they realised that the cost of the materials required was as low as £150. They have made their design freely available with the hopes of making microbiological research more affordable.

Dr Justin Pachebat and Professor Jo Hamilton were asked to help analyse the contents of ‘The Beast’: a 130-tonne fatberg found blocking London’s sewers. In this blog, they discussed what a fatberg is, the challenges of researching something so new (and disgusting!) and what they found inside. Justin and Jo were even on the Channel 4 programme ‘Fat Autopsy: Secrets of the Sewers’.

In what may be one of our most important blogs of the year, Dr Kevin Maringer from the University of Surrey discussed his experiences as a gay man in science and why he thinks it is important that all students and early career researchers to have role models they can identify with.

To celebrate the first ever UN Assembly high-level meeting on tuberculosis, we looked back at the 19th century, when the disease killed as many as one in four people. Since its discovery by Robert Koch, TB research has come a long way, yet still 1.8 billion people are infected worldwide.

This year’s Microbiology Society Annual Conference was a great one. This blog looks back at some of the highlights from Twitter. Another blog that did well this year was by Rebecca Hall on her experience as an Early Career Microbiologist at the Conference.

Plastic pollution has undeniably been at the forefront of the news this year. Since the BBC’s Blue Planet 2 shone a spotlight on the plastic building up in our oceans and killing wildlife, public awareness of the issue has peaked. This blog summarises Kevin O’Connor’s hot topic lecture at the Microbiology Society Annual Conference 2018. If you want to find out more, you can see the full talk here.

This blog saw the launch of a new series on the 12 antimicrobial-resistant microbes that are of most concern to the World Health Organization. We launched during World Antibiotics Awareness week with this blog on Shigella. The series runs alongside an article collection in Microbial Genomics and also includes blogs on Enterobacteriaceae and Salmonella.

In this blog we discuss Streptomyces, a genus of soil bacteria responsible for the production of over fifty antimicrobial medicines. Using Streptomyces as a source of new antibiotic compounds has slowed down in recent years, but with the growing concern around antibiotic resistant superbugs, this area of research is becoming popular once again.

In 2007, Kalai Mathee began a quest to find the first reported use of Pseudomonas aeruginosa PA14; a strain commonly used in pathogenesis research. In this blog, we look back at some of the research that has been published using this strain.

1: Young Microbiologist of the Year Finalists

Courtney Kousser

The Sir Howard Dalton Young Microbiologist of the Year Prize is awarded by the society each year. This year, we met all of the finalists from the four divisions to learn about their research before the event. These profiles from Laura, Katherine, Rute, Stephen, Paula, Freddy, Cathy and, this year’s winner, Courtney, were by far some of our most viewed blog posts.

Thank you to everyone who has contributed to the blog this year and to all of our readers. Here’s to a great 2019!

As we approach the end of 2018, this week on Microbe Post we will be looking back at some of our achievements from the year. Today, we are looking at the Microbiology Society’s journals portfolio and some of the amazing microbiology research that was published in 2018.

In Microbial Genomics, researchers used genetic information to understand the spread of diseases. One paper discussed the genomic epidemiology of Renibacterium salmoninarum, a pathogen that causes bacterial kidney disease in farmed salmon. The paper focused on when the disease was introduced into Chile and how it spread after the first outbreak. Another paper was published describing how resistance to multiple drugs has evolved in the pathogen that causes TB. The researchers studied Mycobacterium tuberculosis isolated from an outbreak in Papua New Guinea.

In an Editorial published in the Journal of General Virology, Dr Derek Gatherer discussed the potential for rapid expansion of the ongoing Ebola outbreak in the Democratic Republic of Congo. Dr Gatherer reflected on the history of the disease in the DRC, and the similarities with the Ebola outbreak that occurred in 2014. Another paper was published discussing how mismatched segments of the influenza virus genome could affect its evolution. The researchers hope that having a better understanding of these processes will help to predict and control future outbreaks of bird flu and swine flu.

In Microbiology, the Editor in Chief co-authored a discussion of ‘Humanity’s deadly microbial foe’, tuberculosis. The Microbe Profile explains why Mycobacterium tuberculosis is such a successful pathogen and what questions still need to be answered to help tackle this disease. In July, a research article by Australian researchers made headlines for the finding that cinnamaldehyde, a component of cinnamon essential oil, can slow spread of the pathogen Pseudomonas aeruginosa.

This year also saw the launch of our new open access journal Access Microbiology. With a changing landscape of academic publishing, we are excited to be able to provide this service to the microbiology community.

To read more of the most read articles across all the Society’s journals, you can see the full collection here. Thanks to everyone that has contributed to our journals this year, whether it is submitting their research, being on an editorial board or peer reviewing articles.

Remember, all journals income is invested back into the Society be it through funding grants, scientific meetings or helping to fund our policy activities. To learn more about our journals or to submit a paper, see here.

With Christmas just around the corner, we thought we’d bring you a festive New to Science! Whilst here in the UK there may not be many white Christmases, there are plenty of microbes being found in the snow. Researchers in China isolated Conyzicola nivalis from a sample of glacial snow from the Zadang Glacier on the Tibetan Plateau. Whilst not the snow you may immediately think of, researchers discovered Muricauda marina in a sample of marine snow. Marine snow is organic material that constantly falls to the depths of the ocean. The composition of marine snow varies, but is mainly dead animals, phytoplankton, protists, and faecal matter; not the kind of snow you’d want to be making snowmen from!

Aurora borealis over Svalbard

Staying with the cold theme, researchers were finding microbial life near the home of Santa Claus himself; the North Pole. With the advent of molecular phylogenetic methods, is has become much easier to study algae found in snow. Using these techniques, researchers were able to isolate Chloromonas arctica, a psychotolerant alga, from snow in the High Arctic. Psychrotolerant organisms are those who can survive in colder temperatures, as apposed to psychrophilic organisms which exclusively grow in cold environments. Researchers also isolated a yellow-orange pigmented bacterium, Subsaxibacter sediminis, from the Arctic permafrost at Midtre Lovénbreen glacier, Svalbard.

Surely nothing’s more festive than a Christmas tree? Three new species of microbes were found in pine forests: Paraburkholderia caseinilytica and Pinisolibacter ravus, both Gram-negative bacteria, were isolated from soil samples from pine forests in Dinghushan Biosphere Reserve, Guangdong Province, China, and Kyonggi University, Republic of Korea, respectively . Promicromonospora callitridis was found within the tree itself; isolated from the root of Callitris preissii, a pine tree endemic to Rottnest Island, Australia.

I’m afraid we couldn’t find all twelve days of Christmas, but we did manage a pear tree, hens, and geese-a-laying. Herbaspirillum piri is a new species of bacteria isolated from a pear tree in Henan Province, China. Megasphaera stantonii, also a new species of bacteria, was found in the cecum of a leghorn chicken. Researchers in Alaska discovered Neisseria arctica, a Gram-negative coccus, in the eggs of the white-fronted goose.

The full papers describing these species are available to journal subscribers, but the abstracts are free to read. Articles can also be purchased individually with the pay-per-view option.

Prof G. Preston: “Mycobacterium smegmatis is used as a model organism to understand the biology of Mycobacterium tuberculosis, the causal agent of tuberculosis (TB) and other mycobacterial pathogens. Thiacetozone (TAC) is an anti-tubercular drug that has been shown to interfere with the synthesis of mycolic acids, long chain fatty acids that form an important component of the cell envelope of mycobacteria…

In this study, the authors resourcefully exploit the ability of TAC to mildly inhibit M. smegmatis growth to provide evidence that TAC inhibits the synthesis of epoxy-mycolates, a family of mycolic acids that form a minor component of the cell envelope of M. smegmatis and other opportunistic pathogens such as Mycobacterium senegalense, Mycobacterium farcinogenes, Mycobacterium peregrinum and Mycobacterium fortuitum. The role of epoxy-mycolates in mycobacterial physiology is undefined, but has been speculated to include adaptation to growth at cooler temperatures.

The paper identifies a specific enzyme responsible for epoxy-mycolate synthesis in M. smegmatis, the mycolic acid methyl transferase (MAMT) MSMEG_1350, and demonstrate that bacteria lacking MSMEG_1350 show increased susceptibility to various stressors at cooler temperatures, supporting this hypothesis. Intriguingly, they also show that bacteria lacking MSMEG_1350 display increased resistance to mycobacteriophages. Collectively, these results show that although epoxy-mycolates are a minor component of the mycobacterial cell envelope, they can make a significant contribution to cell envelope assembly and function.”

Mycobacterium tuberculosis contains uniquely intricate, well characterised fatty acids -mycolic acids- of relevance in mycobacterial viability and pathogenesis; however, equivalent research in other members of the genus, such as Mycobacterium smegmatis, is less characterised.

Our work aims to identify those missing steps in this species. Here, we identified an enzyme leading to the synthesis of epoxy-mycolic acids. A mutant unable to make those molecules was subtly altered in cell wall function and structure, including an unexpected role in resistance to several mycobacterial viruses which would help addressing the nature of the receptors for those viruses.

To access the full paper, click here. All Editor’s Choice articles are free to read.

I am a second year Walsh Fellowship PhD student based in Teagasc Grange and registered at University College Dublin. The title of my project is Understanding of the role of diet, host feed efficiency and genetics on the rumen microbiome and environmental outputs in beef cattle.

The need to feed an ever growing global population while also being required to limit the negative impacts on the environment associated with livestock production is a major challenge for global agriculture. Methane originating from ruminant livestock production is responsible for nearly 40% of global agriculture’s emissions, with cattle identified as the main contributor. Here in Ireland in particular, agriculture is the single largest contributor (~30%) to overall Greenhouse Gas emissions, and it is important to develop and implement abatement strategies through dietary management and breeding tools.

Previously, research has established a link between feed efficiency and methane production whereby cattle that are more feed efficient produce less methane. A group of microbes residing in the rumen, known as methanogens, are responsible for the production of methane. Methane production, or methanogenesis, is an energy inefficient process whereby an estimated 6-12% energy intake of an animal is deflected toward methanogensis. This energy could otherwise contribute to animal performance such as growth or milk production.

My research forms part of the international collaborative project, RumenPredict, which aims to improve our understanding of the role of diet, host genetics, and the rumen microbiome on environmental outputs, including methane and nitrous oxide, and economic traits such as feed efficiency. In other words, the project aims to identify DNA-based biomarkers associated with a rumen microbiome that facilitates greater feed efficiency and less environmental output.

In my PhD, we aim to collect data on over 400 beef cattle over the next 2 years. To measure methane emissions, we have installed two GreenFeed Systems in the Irish Cattle Breeding Federation (ICBF) progeny test centre, where the growth performance of progeny from a variety of beef bulls is evaluated.

The GreenFeed systems allow for estimates of emissions from individual animals in a commercial setting. Animals are tagged with unique RFIDs and as they approach, the RFID tag is read. Then, the air surrounding the animal is extracted and the amount of methane emitted by the animal is measured.

Research by others has shown host control over the rumen microbiome, with the rumen microbial population varying across breeds and indeed between members of the same breed .This suggests there is a genetic influence on rumen microbiome, allowing for the possibility of breeding animals with a more efficient and environmentally friendly rumen microbiome. During my research, I will collect a rumen sample from each animal to identify which microbes are associated with reduced methane emissions and high feed efficiency. In addition, host DNA will also be collected from each animal and genotyped. Genome wide association studies will be performed to identify DNA biomarkers that are correlated with a rumen microbiome that facilitates reduced greenhouse gas emissions and high production efficiency.

In addition to this, we have been investigating the impact diet has on methane production and the rumen microbiome. White clover, along with other legumes, is included in the grazing sward due to their unique ability to fix atmospheric nitrogen. White clover has also shown potential in reducing methane emissions from ruminants, with previous research carried out in Teagasc Moorepark, revealing that dairy cows grazing swards with white clover had reduced emissions of methane per kilogram of dry matter intake (also known as methane yield) when compared to cows grazing perennial ryegrass only. To better understand the effect white clover inclusion in the sward had on the rumen microbiome, we investigated if the difference in methane yield between both groups of dairy cows could be explained by alterations to the microbial population. We used an amplicon sequencing approach, whereby we extracted microbial DNA from rumen samples taken from the cows grazing both swards and generated 16S rRNA amplicon libraries for sequencing on the Illumina MiSeq. Indeed we found that the diet altered the rumen microbiome between the two groups with the abundance of key rumen microbes also varying. Interestingly, we uncovered a reduction in specific methanogens in the rumen microbiome of cows grazing the clover swards.

My day varies quite a bit, particularly when we are measuring methane on a group of cattle using the GreenFeed systems. When methane production is being estimated, I first have to train the animals to become accustomed to using the machines on a regular basis. After this, the cattle are monitored to ensure they are routinely attending the machine. In addition to this, maintenance must be carried on the machines weekly.

If I am not at the ICBF progeny test centre, I could be either analysing the methane data or be in the molecular laboratory extracting microbial DNA from rumen samples and generating 16S rRNA libraries for sequencing. Recently I have just finished analysing the rumen microbial sequence data generated from the clover study and now I am in the process of producing a scientific paper from the results. Also, as part of RumenPredict, we aim to produce guidelines that researchers in the field can follow for best practice. As part of this, we are working on a rumen sequencing standard, containing known quantities of specific rumen microbial DNA which can be included in sequencing analysis for quality control purposes. At the moment, I am both working on our standard and in the process of training a group of cattle to use the GreenFeed.

I am quite lucky in that my PhD both has a production and laboratory element to it allowing me to learn many new skills in production and molecular biology. I love being out on the farm working with the cattle as I get to be outdoors, but equally I love working in the lab.

I choose the topic of my PhD project for a number of reasons. I have an interest in genetics and the genetic element of the project greatly appealed to me. In addition I was attracted to the mitigation potential aspect of the project as, climate change and reducing the impacts all sectors have on the environment is a very topical area.

If we discover DNA based biomarkers that are strongly correlated with the rumen microbiome, feed efficiency and methane production, I would hope they can contribute to both national and international breeding programmes to help breed cattle with a microbiome capable of producing less emissions and harnessing more energy from the feed and thus lead to more sustainable and environmentally friendly beef production.